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Title: Theoretical Investigation of the Enzymatic Phosphoryl Transfer of β-phosphoglucomutase: Revisiting Both Steps of the Catalytic Cycle

Abstract

Enzyme catalyzed phosphate transfer is a part of almost all metabolic processes. Such reactions are of central importance for the energy balance in all organisms and play important roles in cellular control at all levels. Mutases transfer a phosphoryl group while nucleases cleave the phosphodiester linkages between two nucleotides. The subject of our present study is the Lactococcus lactis β-phosphoglucomutase (β-PGM), which effectively catalyzes the interconversion of β-D-glucose-1-phosphate (β-G1P) to β- D-glucose-6-phosphate (β-G6P) and vice versa via stabile intermediate β-D-glucose-1,6-(bis)phosphate (β-G1,6diP) in the presence of Mg2+. In this paper we revisited the reaction mechanism of the phosphoryl transfer starting from the bisphosphate β-G1,6diP in both directions (toward β-G1P and β-G6P) combining docking techniques and QM/MM theoretical method at the DFT/PBE0 level of theory. In addition we performed NEB (nudged elastic band) and free energy calculations to optimize the path and to identify the transition states and the energies involved in the catalytic cycle. Our calculations reveal that both steps proceed via dissociative pentacoordinated phosphorane, which is not a stabile intermediate but rather a transition state. In addition to the Mg2+ ion, Ser114 and Lys145 also play important roles in stabilizing the large negative charge on the phosphate through strong coordinationmore » with the phosphate oxygens and guiding the phosphate group throughout the catalytic process. The calculated energy barrier of the reaction for the β-G1P to β-G1,6diP step is only slightly higher than for the β-G1,6diP to β-G6P step (16.10 kcal mol-1 versus 15.10 kcal mol-1) and is in excellent agreement with experimental findings (14.65 kcal mol-1).« less

Authors:
; ;
Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Org.:
USDOE
OSTI Identifier:
1097947
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
Journal of Molecular Modeling, 18(7):3169–3179
Additional Journal Information:
Journal Name: Journal of Molecular Modeling, 18(7):3169–3179
Country of Publication:
United States
Language:
English
Subject:
Environmental Molecular Sciences Laboratory

Citation Formats

Elsasser, Brigitta M., Dohmeier-Fischer, Silvia, and Fels, Gregor. Theoretical Investigation of the Enzymatic Phosphoryl Transfer of β-phosphoglucomutase: Revisiting Both Steps of the Catalytic Cycle. United States: N. p., 2012. Web. doi:10.1007/s00894-011-1344-5.
Elsasser, Brigitta M., Dohmeier-Fischer, Silvia, & Fels, Gregor. Theoretical Investigation of the Enzymatic Phosphoryl Transfer of β-phosphoglucomutase: Revisiting Both Steps of the Catalytic Cycle. United States. doi:10.1007/s00894-011-1344-5.
Elsasser, Brigitta M., Dohmeier-Fischer, Silvia, and Fels, Gregor. Thu . "Theoretical Investigation of the Enzymatic Phosphoryl Transfer of β-phosphoglucomutase: Revisiting Both Steps of the Catalytic Cycle". United States. doi:10.1007/s00894-011-1344-5.
@article{osti_1097947,
title = {Theoretical Investigation of the Enzymatic Phosphoryl Transfer of β-phosphoglucomutase: Revisiting Both Steps of the Catalytic Cycle},
author = {Elsasser, Brigitta M. and Dohmeier-Fischer, Silvia and Fels, Gregor},
abstractNote = {Enzyme catalyzed phosphate transfer is a part of almost all metabolic processes. Such reactions are of central importance for the energy balance in all organisms and play important roles in cellular control at all levels. Mutases transfer a phosphoryl group while nucleases cleave the phosphodiester linkages between two nucleotides. The subject of our present study is the Lactococcus lactis β-phosphoglucomutase (β-PGM), which effectively catalyzes the interconversion of β-D-glucose-1-phosphate (β-G1P) to β- D-glucose-6-phosphate (β-G6P) and vice versa via stabile intermediate β-D-glucose-1,6-(bis)phosphate (β-G1,6diP) in the presence of Mg2+. In this paper we revisited the reaction mechanism of the phosphoryl transfer starting from the bisphosphate β-G1,6diP in both directions (toward β-G1P and β-G6P) combining docking techniques and QM/MM theoretical method at the DFT/PBE0 level of theory. In addition we performed NEB (nudged elastic band) and free energy calculations to optimize the path and to identify the transition states and the energies involved in the catalytic cycle. Our calculations reveal that both steps proceed via dissociative pentacoordinated phosphorane, which is not a stabile intermediate but rather a transition state. In addition to the Mg2+ ion, Ser114 and Lys145 also play important roles in stabilizing the large negative charge on the phosphate through strong coordination with the phosphate oxygens and guiding the phosphate group throughout the catalytic process. The calculated energy barrier of the reaction for the β-G1P to β-G1,6diP step is only slightly higher than for the β-G1,6diP to β-G6P step (16.10 kcal mol-1 versus 15.10 kcal mol-1) and is in excellent agreement with experimental findings (14.65 kcal mol-1).},
doi = {10.1007/s00894-011-1344-5},
journal = {Journal of Molecular Modeling, 18(7):3169–3179},
number = ,
volume = ,
place = {United States},
year = {2012},
month = {7}
}